Integrating transformer-based machine learning with SERS technology for the analysis of hazardous pesticides in spinach.

This study introduces an innovative strategy for the rapid and accurate identification of pesticide residues in agricultural products by combining surface-enhanced Raman spectroscopy (SERS) with a state-of-the-art transformer model, termed SERSFormer. Gold-silver core-shell nanoparticles were synthesized and served as high-performance SERS substrates, which possess well-defined structures, uniform dispersion, and a core-shell composition with an average diameter of 21.44 ± 4.02 nm, as characterized by TEM-EDS. SERSFormer employs sophisticated, task-specific data processing techniques and CNN embedders, powered by an architecture features weight-shared multi-head self-attention transformer encoder layers. The SERSFormer model demonstrated exceptional proficiency in qualitative analysis, successfully classifying six categories, including five pesticides (coumaphos, oxamyl, carbophenothion, thiabendazole, and phosmet) and a control group of spinach data, with 98.4% accuracy. For quantitative analysis, the model accurately predicted pesticide concentrations with a mean absolute error of 0.966, a mean squared error of 1.826, and an R2 score of 0.849. This novel approach, which combines SERS with machine learning and is supported by robust transformer models, showcases the potential for real-time pesticide detection to improve food safety in the agricultural and food industries.

Acidic electrolyzed-oxidizing water treatment mitigated the disease progression in Phomopsis longanae Chi-infected longans by modulating ROS and membrane lipid metabolism.

Postharvest harmful pathogenic infestation leads to rapid decay in longan fruit. Compared with P. longanae-infected longans, AEOW alleviated fruit disease severity and diminished the O2-. production rate and MDA content. It also increased APX, CAT, and SOD activities, delayed the decrease in the levels of GSH and AsA, as well as the reducing power and DPPH radical scavenging ability, which resulted in a decline in membrane lipid peroxidation in P. longanae-infected longans. Additionally, AEOW reduced LOX, lipase, PI-PLC, PC-PLC, and PLD activities, maintained higher levels of PC, PI, IUFA, USFAs, and U/S, while reducing levels of PA, DAG, SFAs, and CMP. These effects alleviated membrane lipid degradation and peroxidation in P. longanae-infected longans. Consequently, AEOW effectively maintained membrane integrity via improving antioxidant capacity and suppressing membrane lipid peroxidation. This comprehensive coordination of ROS and membrane lipid metabolisms improved fruit resistance and delayed disease development in longans.

Comparative transcriptome and metabolome reveal the role of acidic electrolyzed oxidizing water in improving postharvest disease resistance of longan fruit.

Acidic electrolyzed oxidizing water (AEOW) was applied to suppress disease development and maintain good quality of fresh fruit. However, the involvement of AEOW in improving disease resistance of fresh longan remains unknown. Here, transcriptomic and metabolic analyses were performed to compare non-treated and AEOW-treated longan during storage. The transcriptome analysis showed AEOW-induced genes associated with phenylpropanoid and flavonoid biosynthesis. The metabolome analysis found the contents of coumarin, phenolic acid, and tannin maintained higher levels in AEOW-treated longan than non-treated longan. Moreover, the weighted correlation network analysis (WGCNA) was performed to identify hub genes, and a gene-metabolite correlation network associated with AEOW-improved disease resistance in longan was constructed by the co-analysis of transcriptomics and metabolomics. These findings identified a series of important genes and metabolites involving in AEOW-induced disease resistance of longan fruit, expanding our knowledges on fruit disease resistance and quality maintenance at the transcript and metabolic levels.

Facile synthesis of gold nanostars for the duplex detection of pesticide residues in grapes using SERS.

In recent years, concerns have been raised regarding the contamination of grapes with pesticide residues. As consumer demand for safer food products grows, regular monitoring of pesticide residues in food has become essential. This study sought to develop a rapid and sensitive technique for detecting two specific pesticides (phosmet and paraquat) present on the grape surface using the surface-enhanced Raman spectroscopy (SERS) method. Gold nanostars (AuNS) particles were synthesized, featuring spiky tips that act as hot spots for localized surface plasmon resonance, thereby enhancing Raman signals. Additionally, the roughened surface of AuNS increases the surface area, resulting in improved interactions between the substrate and analyte molecules. Prominent Raman peaks of mixed contaminants were acquired and used to characterize and quantify the pesticides. It was observed that the SERS intensity of the Raman peaks changed in proportion to the concentration ratio of phosmet and paraquat. Moreover, AuNS exhibited superior SERS enhancement compared to gold nanoparticles. The results demonstrate that the lowest detectable concentration for both pesticides on grape surfaces is 0.5 mg/kg. These findings suggest that SERS coupled with AuNS constitutes a practical and promising approach for detecting and quantifying trace contaminants in food. PRACTICAL APPLICATION: This research established a novel surface-enhanced Raman spectroscopy (SERS) method coupled with a simplified extraction protocol and gold nanostar substrates to detect trace levels of pesticides in fresh produce. The detection limits meet the maximum residue limits set by the EPA. This substrate has great potential for rapid measurements of chemical contaminants in foods.

Hydrogen peroxide induced changes in the levels of disease-resistant substances and activities of disease-resistant enzymes in relation to the storability of longan fruit.

The influences of hydrogen peroxide (H2O2) on the storability and metabolism of disease-resistant substances in fresh longan were investigated. Compared to the control samples, H2O2-treated longan exhibited a higher index of fruit disease, pericarp browning, and pulp breakdown, a higher rate of fruit weight loss, but lower chromaticity values (L*, a* and b*) in pericarp appearance, and a lower commercially acceptable fruit rate. Additionally, H2O2-treated longan showed a lower lignin content, lower activities of enzymes including phenylalnine ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumaryl coenzyme A ligase (4-CL), cinnamate dehydrogenase (CAD), peroxidase (POD), chitinase (CHI), and ß-1,3-glucanase (GLU). These data collectively suggest that H2O2 negatively impacted the storability of fresh longan. This can be attributed to H2O2's role in reducing the levels of disease-resistant substances and suppressing the activities of disease-resistant enzymes, implying that H2O2 reduced the postharvest storability of longan by compromising its disease resistance.

The metabolism of membrane lipid participates in the occurrence of chilling injury in cold-stored banana fruit.

Banana fruit is highly vulnerable to chilling injury (CI) during cold storage, which results in quality deterioration and commodity reduction. The purpose of this study was to investigate the membrane lipid metabolism mechanism underlying low temperature-induced CI in banana fruit. Chilling temperature significantly induced CI symptoms in banana fruit, compared to control temperature (22 °C). Using physiological experiments and transcriptomic analyses, we found that chilling temperature (7 °C) increased CI index, malondialdehyde content, and cell membrane permeability. Additionally, chilling temperature upregulated the genes encoding membrane lipid-degrading enzymes, such as lipoxygenase (LOX), phospholipase D (PLD), phospholipase C (PLC), phospholipase A (PLA), and lipase, but downregulated the genes encoding fatty acid desaturase (FAD). Moreover, chilling temperature raised the activities of LOX, PLD, PLC, PLA, and lipase, inhibited FAD activity, lowered contents of unsaturated fatty acids (USFAs) (γ-linolenic acid and linoleic acid), phosphatidylcholine, and phosphatidylinositol, but retained higher contents of saturated fatty acids (SFAs) (stearic acid and palmitic acid), free fatty acids, phosphatidic acid, lysophosphatidic acid, diacylglycerol, a lower USFAs index, and a lower ratio of USFAs to SFAs. Together, these results revealed that chilling temperature-induced chilling injury of bananas were caused by membrane integrity damage and were associated with the enzymatic and genetic manipulation of membrane lipid metabolism. These activities promoted the degradation of membrane phospholipids and USFAs in fresh bananas during cold storage.

CRISPR-Cas12a Biosensor Array for Ultrasensitive Detection of Unamplified DNA with Single-Nucleotide Polymorphic Discrimination.

Quantitative polymerase chain reaction as a powerful tool for DNA detection has been pivotal to a vast range of applications, including disease screening, food safety assessment, environmental monitoring, and many others. However, the essential target amplification step in combination with fluorescence readout poses a significant challenge to rapid and streamlined analysis. The discovery and engineering of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) technology have recently paved the way for a novel approach to nucleic acid detection, but the majority of current CRISPR-mediated DNA detection platforms are limited by insufficient sensitivity and still require target preamplification. Herein, we report a CRISPR-Cas12a-mediated graphene field-effect transistor (gFET) array, named CRISPR Cas12a-gFET, for amplification-free, ultrasensitive, and reliable detection of both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) targets. CRISPR Cas12a-gFET leverages the multiturnover trans-cleavage activity of CRISPR Cas12a for intrinsic signal amplification and ultrasensitivity of gFET. As demonstrated, CRISPR Cas12a-gFET achieves a limit of detection of 1 aM for the ssDNA human papillomavirus 16 synthetic target and 10 aM for the dsDNA Escherichia coli plasmid target without target preamplification. In addition, an array of 48 sensors on a single 1.5 cm × 1.5 cm chip is employed to improve data reliability. Finally, Cas12a-gFET demonstrates the capability to discriminate single-nucleotide polymorphisms. Together, the CRISPR Cas12a-gFET biosensor array provides a detection tool for amplification-free, ultrasensitive, reliable, and highly specific DNA detections.

The effect of ε-poly-l-lysine treatment on molecular, physiological and biochemical indicators related to resistance in longan fruit infected by Phomopsis longanae Chi.

Postharvest longan fruits are subjected to Phomopsis longanae Chi (P. longanae) infection that lead to fruit quality deterioration. We hypothesized that ε-poly-l-lysine (ε-PL) could enhance fruit disease resistance in longans. Through physiological and transcriptomic analyses, the results showed that, compared to P. longanae-infected longan fruit, ε-PL + P. longanae treatment reduced the disease development of longan fruits. Additionally, ε-PL + P. longanae treatment increased the contents of disease-resistant substances (lignin and H2O2) and the activities of disease-resistance enzymes (CHI, PAL, PPO, C4H, CAD, GLU, 4CL, and POD). Furthermore, the expressions of genes relevant to the phenylpropanoid biosynthesis pathway and plant-pathogen interaction pathway (Rboh, FLS2, WRKY29, FRK1, and PR1) were up-regulated by ε-PL + P. longanae treatment. These findings demonstrated that ε-PL treatment inhibited the disease development of postharvest longan fruits were associated with the increased accumulation of disease-resistant related substances, as well as the raised activities and genes expressions of disease-resistance related enzymes.

DNP and ATP regulate the breakdown occurrence in the pulp of Phomopsis longanae Chi-infected longan fruit through modulating the metabolism of membrane lipid.

This study aimed to illustrate how DNP and ATP affected the pulp breakdown occurrence in P. longanae-infected longan and their relationship with the membrane lipid metabolism. Compared with P. longanae-inoculated samples, the pulp of DNP-treated P. longanae-infected longan exhibited higher cellular membrane permeability, breakdown index, activities of PI-PLC, PLD, PC-PLC, LOX, and lipase, and values of SFAs, PA, and DAG, while lower levels of PI, PC, USFAs, IUFA and U/S. However, the opposite findings were observed in ATP-treated P. longanae-infected longan. The data manifested that DNP-increased the pulp breakdown occurrence in P. longanae-inoculated samples was due to the elevated MLDEs activities that reduced the contents of phospholipids (PI, PC) and USFAs, disrupting the cell membrane structures. Nevertheless, ATP decreased the pulp breakdown occurrence in P. longanae-inoculated samples, which was ascribed to the reduced MLDEs activities that raised phospholipids (PI, PC) and USFAs contents, thus maintaining the cell membrane structures.

CRISPR-Cas Biochemistry and CRISPR-Based Molecular Diagnostics.

Polymerase chain reaction (PCR)-based nucleic acid testing has played a critical role in disease diagnostics, pathogen surveillance, and many more. However, this method requires a long turnaround time, expensive equipment, and trained personnel, limiting its widespread availability and diagnostic capacity. On the other hand, the clustered regularly interspaced short palindromic repeats (CRISPR) technology has recently demonstrated capability for nucleic acid detection with high sensitivity and specificity. CRISPR-mediated biosensing holds great promise for revolutionizing nucleic acid testing procedures and developing point-of-care diagnostics. This review focuses on recent developments in both fundamental CRISPR biochemistry and CRISPR-based nucleic acid detection techniques. Four ongoing research hotspots in molecular diagnostics-target preamplification-free detection, microRNA (miRNA) testing, non-nucleic-acid detection, and SARS-CoV-2 detection-are also covered.

Acidic electrolyzed water treatment suppresses Phomopsis longanae Chi-induced the decreased storability and quality properties of fresh longans through modulating energy metabolism.

Longan fruit loses its market value rapidly due to postharvest pathogenic infestation and quality deterioration. Here, we hypothesized that acidic electrolyzed water (AEW) could maintain higher quality of P. longanae-inoculated longans via regulating energy metabolism. Results indicated that AEW reduced fruit disease index and decay incidence. Significantly, AEW treatment retained higher levels of ATP, ADP, and energy charge, and higher activities of Ca2+-ATPase, Mg2+-ATPase, and H+-ATPase in the membranes of plasma, vacuole, and mitochondria, which maintained the structural and functional integrity of cell membrane. Furthermore, indirectly sustaining cell membrane function via AEW treatment could maintain the storability and quality properties of longans, including keeping higher values of color chromaticity (L*, a*, and b*), higher amounts of vitamin C, total soluble solids, sucrose, and total soluble sugars, lower titratable acid and reducing sugar contents. This work elucidated the potential regulation of AEW on the balance of energy metabolism and fruit quality.

Comparison between two cultivars of longan fruit cv. 'Dongbi' and 'Fuyan' in the metabolisms of lipid and energy and its relation to pulp breakdown.

This work studied the difference in pulp breakdown between two cultivars of longan cv. 'Dongbi' and 'Fuyan' from the aspect of metabolisms of lipid and energy. The results reflected that, compared to 'Fuyan' longan, 'Dongbi' longan had higher levels of energy charge, U/S and IUFA, and higher amounts of USFA, PC, PI, ATP and ADP. Moreover, 'Dongbi' longan exhibited lower levels of SFA, PA, AMP and cell membrane permeability. Also, lower PLD, LOX and lipase activities, but higher ATPase activity, lower pulp breakdown index, and better pulp appearance were exhibited in 'Dongbi' longan. These data revealed that the mitigated pulp breakdown in 'Dongbi' longan was due to the comprehensive coordination of metabolisms in lipid and energy through maintaining a higher level of energy, a higher unsaturation degree of fatty acids, delaying the degradation of phospholipids, and better retaining the membrane structural integrity of microsome and entire cell.

Preparation and Characterization of Boza Enriched with Nonfat Dry Milk and Its Impact on the Fermentation Process.

Boza is an indigenous, traditional, low-alcohol and highly viscous beverage prepared by fermenting cereals. Its thick and gel-like consistency make it suitable for consumption via spoon. Although boza is a nutritious beverage, its protein content is very low (<2%). A new type of boza was developed by incorporating nonfat dry milk (NFDM) to elevate the protein content of the beverage. Different NFDM amounts (10 to 40% w/v) were added to determine the best concentration and fermentation time based on the refractive index and pH values at room temperature (0-48 h). The best sample was further characterized by rheological analyses and Fourier transform infrared (FTIR) spectroscopy. The sample with 10% NFDM was the best, as fermentation was successfully performed, and further addition of NFDM increased the initial pH. The refractive index and pH decreased from 21.9 ± 0.1 to 11.8 ± 0.1 and 5.77± 0.50 to 4.09 ± 0.35 during fermentation, respectively. The samples exhibited shear-thinning, solid-like behavior, and a gel-like structure. FTIR analysis by independent modeling of class analogy (SIMCA) demonstrated that unfermented slurry and the fermented product could be effectively differentiated. With the addition of 10% NFDM, the increase in the protein content of the boza medium became significant.

Duplex detection of foodborne pathogens using a SERS optofluidic sensor coupled with immunoassay.

Herein, we developed a surface-enhanced Raman spectroscopy (SERS) optofluidic sensor coupled with immunoprobes to simultaneously separate and detect the foodborne pathogens, Escherichia coli O157:H7, and Salmonella in lettuce and packed salad. The method consists of three steps of (i) enrichment to enhance detection sensitivity, (ii) selective separation and labelling of target bacteria by their specific antibody-bearing SERS-nanotags and (iii) detection of tagged bacterial cells using SERS within a hydrodynamic flow-focusing SERS optofluidic device, where even low counts of bacterial cells were detectable in the very thin-film-like sample stream. SERS-nanotags consisted of different Raman reporter molecules, representing each species, i.e., the detection of Raman reporter confirms the presence of the target pathogen. The anti-E. coli antibody used in this study functions against all strains of E. coli O157:H7 and the anti-Salmonella antibody used in this work acts on a wide range of Salmonella enterica strains. Bacterial counts of 1000, 100, and 10 CFU/ 200 g sample were successfully detected after only 15 min enrichment. Our method showed a very low detection limit value of 10 CFU/ 200 g sample for the bacterial mixture in both lettuce and packed salad, proving the efficiency and high sensitivity of our method to detect multiple pathogens in the food samples. The total analysis time, including sample preparation for simultaneous detection of multiple bacteria, was estimated to be 2 h, which is much less than the time required in conventional methods. Hence, our proposed protocol is considered a promising rapid and efficient approach for pathogen screening of food samples.

DNP and ATP modulate the developments of pulp softening and breakdown in Phomopsis longanae Chi-infected fresh longan through regulating the cell wall polysaccharides metabolism.

Compared with P. longanae-infected longan, 2, 4-dinitrophenol (DNP) treatment for P. longanae-infected longan displayed the lower levels of pulp firmness, cell wall materials, ionic-soluble pectin, covalent-soluble pectin, hemicellulose, or cellulose, but the higher amount of water-soluble pectin, the higher activities of cell wall-degrading enzymes (CWDEs) (PG, ß-Gal, PME, Cx, and XET), and the higher transcript levels of CWDEs-related genes (DlPG1, DlPG2, Dlß-Gal1, DlPME1, DlPME2, DlPME3, DlCx1, and DlXET30). On the contrary, ATP treatment for P. longanae-infected longan exhibited opposite effects. The above results imply that DNP accelerated P. longanae-induced pulp softening and breakdown of fresh longan, which was because DNP up-regulated the transcript levels of CWDEs-related genes, enhanced the CWDEs activities, and accelerated the degradation of cell wall polysaccharides (CWP). However, ATP suppressed longan pulp softening and breakdown caused by P. longanae, because ATP down-regulated the transcript levels of CWDEs-related genes, lowered the CWDEs activities, and reduced the CWP degradation.

γ-Aminobutyric acid treatment reduces chilling injury and improves quality maintenance of cold-stored Chinese olive fruit.

This study developed a useful technique to maintain quality and mitigate chilling injury of cold-stored Chinese olive fruit. Influence of dose (0, 0.5, 1.0, 1.5, 2.0 mM) of γ-aminobutyric acid (GABA) on the quality attributes and chilling damage of Chinese olive when stored at 2 °C for 100 d was investigated. Compared to control samples, GABA-treated fruit displayed lower chilling injury index, cell membrane permeability, and weight loss percentage, but higher hue angle h° value, higher levels of chlorophyll, total soluble sugar, sucrose, total soluble solids, titratable acid, and tannin, and 1.0 mM GABA is the optimal concentration to retain the quality attributes and reduce the chilling injury of Chinese olive fruit during cold storage.

Phomopsis longanae Chi causing the pulp breakdown of fresh longan fruit through affecting reactive oxygen species metabolism.

Phomopsis longanae Chi is a crucial pathogen causing fruit spoilage in postharvest fresh longan. The influence of P. longanae invasion with a suspension containing 1 × 104 P. longanae spores per mL on the breakdown occurrence and ROS metabolism in pulp of longan cv. Fuyan during storage at 28 °C was explicated. Compared to control group, more severe development of pulp breakdown (PB), higher PB index, O2 -. generation rate, H2O2 and MDA content, but lower SOD, APX and CAT activities, GSH, AsA, flavonoid and total phenolics amounts, ability of scavenging DPPH radical, and reducing power were displayed in the pulp of P. longanae-infected fruit during days 0-5. In this context, P. longanae induced breakdown of longan pulp by reducing the scavenging ability of ROS and increasing the cumulation of ROS, thereby enhancing the structural collapse and lipid peroxidation of cell membrane, which were responsible for the PB of harvested longans.

Bioanalytical approaches for the detection, characterization, and risk assessment of micro/nanoplastics in agriculture and food systems.

This review discusses the most recent literature (mostly since 2019) on the presence and impact of microplastics (MPs, particle size of 1 µm to 5 mm) and nanoplastics (NPs, particle size of 1 to 1000 nm) throughout the agricultural and food supply chain, focusing on the methods and technologies for the detection and characterization of these materials at key entry points. Methods for the detection of M/NPs include electron and atomic force microscopy, vibrational spectroscopy (FTIR and Raman), hyperspectral (bright field and dark field) and fluorescence imaging, and pyrolysis-gas chromatography coupled to mass spectrometry. Microfluidic biosensors and risk assessment assays of MP/NP for in vitro, in vivo, and in silico models have also been used. Advantages and limitations of each method or approach in specific application scenarios are discussed to highlight the scientific and technological obstacles to be overcome in future research. Although progress in recent years has increased our understanding of the mechanisms and the extent to which MP/NP affects health and the environment, many challenges remain largely due to the lack of standardized and reliable detection and characterization methods. Most of the methods available today are low-throughput, which limits their practical application to food and agricultural samples. Development of rapid and high-throughput field-deployable methods for onsite screening of MP/NPs is therefore a high priority. Based on the current literature, we conclude that detecting the presence and understanding the impact of MP/NP throughout the agricultural and food supply chain require the development of novel deployable analytical methods and sensors, the combination of high-precision lab analysis with rapid onsite screening, and a data hub(s) that hosts and curates data for future analysis.

Amelioration of chilling injury and enhancement of quality maintenance in cold-stored guava fruit by melatonin treatment.

The influence of melatonin treatment on the quality and chilling injury of guavas during storage at 4 ± 1 °C were evaluated. Compared with control group, fruit of guava cv. Xiguahong exposed to various concentrations (50, 100, 150, and 200 µmol/L) of melatonin showed a significantly lower fruit respiration rate, weight loss, cell membrane permeability, and chilling injury index, but a higher commercially acceptable fruit rate, higher peel L*, h° value, and chlorophyll content. Melatonin treatment also delayed the decreases of fruit firmness, sucrose, total soluble sugar, vitamin C, titratable acidity, and total soluble solids. These data indicate that melatonin treatment could increase chilling tolerance and retain quality of cold-stored guavas. Among various concentrations of melatonin treatment, 100 µmol/L melatonin-treated guavas showed the preferable quality properties and lowest chilling injury index. Thus, melatonin may be a novel method of postharvest handling to enhance cold resistance and extend storage-life of cold-stored guava fruit.

ε-Poly-l-Lysine Enhances Fruit Disease Resistance in Postharvest Longans (Dimocarpus longan Lour.) by Modulating Energy Status and ATPase Activity.

ε-poly-l-lysine (ε-PL) holds a strong antibacterial property and is widely used for food preservation. However, the application of ε-PL to enhance fruit disease resistance in postharvest longans (Dimocarpus longan Lour.) has not been explored. The objective of this study was to explore the impact of ε-PL treatment on disease occurrence and energy metabolism of longans infected with Phomopsis longanae Chi (P. longanae). It was found that, in comparison with P. longanae-inoculated longans, ε-PL could decrease the fruit disease index and adenosine monophosphate (AMP) content, increase the amounts of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and energy charge, and enhance the activities of adenosine triphosphatase (ATPase) (such as H+-, Mg2+-, and Ca2+-ATPase) in the mitochondria, protoplasm, and vacuole. The results suggest that the higher levels of ATPase activity and energy status played essential roles in disease resistance of postharvest longan fruit. Therefore, the ε-PL treatment can be used as a safe and efficient postharvest method to inhibit the disease occurrence of longan fruit during storage at room temperature.